Article
Immunology
Jiachun Su, Xu Han, Xiaogang Xu, Wenchao Ding, Ming Li, Weiqin Wang, Mi Tian, Xiyuan Chen, Binbin Xu, Zhongqing Chen, Jinyi Yuan, Xiaohua Qin, Dongfang Lin, Ruilan Wang, Ye Gong, Liping Pan, Jun Wang, Minggui Wang
Summary: The clinical value of using metagenomic next-generation sequencing (mNGS) to detect tumors in patients with suspected infections has been demonstrated.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Oncology
Jasmine H. Francis, Allison L. Richards, Diana L. Mandelker, Michael F. Berger, Michael F. Walsh, Ira J. Dunkel, Mark T. A. Donoghue, David H. Abramson
Summary: By sequencing enucleated retinoblastoma specimens, this study found correlations between vitreous seeding and copy number variations, as well as between BCOR mutations and propensity for metastasis. Additionally, a portion of patients were found to have additional germline mutations in other cancer-related genes.
Article
Biology
Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov
Summary: CNVpytor is an extension of CNVnator that improves performance and functionality, allowing for filtering, annotation, and merging of CNV calls across multiple samples. Its modular architecture enables use in shared and cloud environments, and data can be exported to JBrowse for visualization and analysis.
Article
Biochemical Research Methods
Edith M. Ross, Kerstin Haase, Peter Van Loo, Florian Markowetz
Summary: The asmultipcf algorithm presented in this study allows allele-specific segmentation of multiple samples, inferring private and shared segment boundaries of phylogenetically related samples. This provides a new tool and method for further research on tumor evolution.
Article
Biotechnology & Applied Microbiology
Tong Zhang, Jinxin Dong, Hua Jiang, Zuyao Zhao, Mengjiao Zhou, Tianting Yuan
Summary: This study proposes a new method, CNV-PCC, for detecting copy number variations (CNVs). By utilizing split read signals and a segmentation strategy, CNV-PCC improves the identification capabilities for low copy number duplications and small CNVs. The analysis of simulated data and real sequencing samples demonstrates that CNV-PCC outperforms other methods in sensitivity, F1-score, and breakpoint accuracy.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Oncology
Woosuk Choi, Joseph Kyu-hyung Park, Seung Geun Song, Baek-kyu Kim
Summary: Although epidermoid cysts are usually benign, they rarely develop into cancerous lesions. A 36-year-old male presented with a cystic mass on his left flank since childhood. Based on medical history and CT scan, the lesion was suspected to be an epidermoid cyst and was excised. Histopathological evaluation revealed poorly differentiated carcinoma with squamoid and basaloid differentiation, indicating a strong possibility of carcinoma arising from an epidermal cyst. Next-generation sequencing using TruSight oncology 500 assay showed copy number variation of ATM and CHEK1 genes.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemical Research Methods
Xinping Fan, Guanghao Luo, Yu S. Huang
Summary: This study presents Accucopy, a method for inferring total copy numbers (TCNs) and allele-specific copy numbers (ASCNs) from challenging low-purity and low-coverage tumor samples. Accucopy utilizes robust statistical techniques and models such as the tiered Gaussian mixture model, expectation-maximization algorithm, and sparse Bayesian learning, outperforming other methods in simulated and real sequencing samples.
BMC BIOINFORMATICS
(2021)
Article
Immunology
Liuqing Yang, Ling Peng, Ke Yuan, Kanru Cai, Cheng Feng, Gendong Yang, Shunyao Wang, Xiuyun Zhu, Jieyun Zhang, Fuxiang Wang, Hongzhou Lu
Summary: We reported a case of infective endocarditis caused by Mycobacterium kansasii in a 45-year-old male patient with fever and decompensated cirrhosis. Metagenomic next-generation sequencing (mNGS) was used to analyze the genome sequences of both the host and microbe, revealing the presence of M. kansasii sequences in peripheral blood samples. However, the patient's condition deteriorated, leading to his demise before heart surgery. Nevertheless, mNGS could be a novel approach for diagnosing M. kansasii infection when blood culture and pathology results are unavailable.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Brendan O'Fallon, Jacob Durtschi, Ana Kellogg, Tracey Lewis, Devin Close, Hunter Best
Summary: This study proposes two algorithmic adaptations to improve the accuracy of CNV detection in a Hidden Markov Model (HMM) context. First, it improves the accuracy by computing target- and copy number-specific emission distributions. Second, it enhances the sensitivity for small CNV calls using the Pointwise Maximum a posteriori (PMAP) HMM decoding procedure. The prototype implementation, called Cobalt, shows similar sensitivity to other CNV detection tools but significantly reduces false positive detections.
BMC BIOINFORMATICS
(2022)
Article
Biotechnology & Applied Microbiology
Xinghao Chen, Yan Dong, Yali Huang, Jianmin Fan, Minsheng Yang, Jun Zhang
Summary: This study conducted genome resequencing of transgenic poplar 741 line Pb29, identifying two T-DNA insertion sites without chromosomal rearrangement. It was found that Pb29 genome only contains the BtCry1AC gene, with minimal impact on the expression levels of surrounding genes.
Article
Biochemistry & Molecular Biology
Andrey Kechin, Ulyana Boyarskikh, Viktoriya Borobova, Evgeniy Khrapov, Sergey Subbotin, Maxim Filipenko
Summary: This study developed a new tool, called BRACNAC, for detecting CNVs and CNAs in the BRCA1 and BRCA2 genes. The tool showed high sensitivity and specificity and could be applied to NGS data of different origins. The study also identified the limitations of the tool.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Xia Zhang, Qingyan Huang, Zhikang Yu, Heming Wu
Summary: This study aimed to explore the relationship between miscarriage and stillbirth with copy number variations (CNVs) by analyzing 659 fetal samples. Results showed 48.86% of cases had chromosomal abnormalities, with numerical abnormalities increasing with maternal age, and structural abnormalities differing significantly among age groups. Numerical chromosomal abnormalities also decreased with increasing gestational age of the fetuses.
JOURNAL OF GENE MEDICINE
(2021)
Article
Transplantation
M. Adela Mansilla, Ramakrishna R. Sompallae, Carla J. Nishimura, Anne E. Kwitek, Mycah J. Kimble, Margaret E. Freese, Colleen A. Campbell, Richard J. Smith, Christie P. Thomas
Summary: Genetic testing was found to be valuable in the evaluation of renal patients, with a high diagnostic rate in patients and the potential to change clinical diagnosis. The study highlights the importance of incorporating broad genetic testing in the management of kidney diseases.
NEPHROLOGY DIALYSIS TRANSPLANTATION
(2021)
Article
Biology
Xiya Zhou, Xiangbin Chen, Yulin Jiang, Qingwei Qi, Na Hao, Chengkun Liu, Mengnan Xu, David S. Cram, Juntao Liu
Summary: This study introduces a rapid CNV-sequencing method for clinical prenatal diagnosis, demonstrating its reliability, accuracy, and reproducibility in detecting a range of common chromosomal abnormalities. Clinical testing confirmed its effectiveness in identifying known chromosome disorders in prenatal samples, suggesting its potential for widespread application in NGS-based diagnostic laboratories.
Article
Biotechnology & Applied Microbiology
Xikang Feng, Lingxi Chen
Summary: This study proposes a new tool, SCSilicon, that efficiently generates single-cell DNA reads and automatically creates genomic aberrations for the development and benchmarking of single-cell CNV callers. The most robust single-cell CNV caller, SCYN, was identified through manual inspection of synthetic variations and a sanity check.